Come on now, you have to be joking?
Rossi and Burgess have been with Ducati since November 2010 - 20 months - and you're saying they still don't understand it? It's a motorcycle, it has handlebars, an engine, wheels and suspension. You ride it, see how it behaves, change things with set-up to see if you can get it to ride how you want it to. If not, you feedback to engineers and say I'd like it to do this or that. They, hopefully, make whatever changes and off you go again.
What difference does it make if it is V4, in-line 4 or V5? I'd wager that if they didn't tell the rider what the engine configuration was, they'd never know.
Rossi had no problem going from a 500 2-stroke to a V5 4-stroke I recall. What experience did they have with V5 4-strokes? - none.
Then to Yamaha and an in-line 4. Again, no previous experience but no problem setting the bike up.
So why the problem at Ducati.
Tyres is a good bet (yes Benny, tyres again....) At Honda and Yamaha, they could have the tyres made to suit the bike. Now they can't and they are stuck because they can't set the bike up to suit the tyre. They aren't alone. And both the Honda and Yamaha at that time were very good bikes.
To say they were exploring all possible ways of setting the bike up like a Yamaha is being kind. They were directionless and lost. Ducati reacted at Jerez, following his Qatar outburst and told him to use Hayden's settings as once again, he was lost in practise and Hayden was up at the sharp end, proving that there is performance in the bike. He used the settings for the race and the improvement was apparent. He's been using them since (as a basis) To say they are Ducati default settings is being unkind to Hayden. He goes his own way with set-up and was doing a better job. You can't say that they were the known settings to favour the GP12 as it was only one race old at that point and in pre-season testing they were both down the lap charts (when times did actually mean something) Hayden found something that worked, Rossi couldn't. The corner that has been turned was the one they were told to follow Hayden around, not one they turned themselves. Events also suggest that this year's tyres may be suiting the bike better as well.
Why is there always a reluctance to accept that Rossi is not this perfect being that has the answer to everything. Very good rider yes, but just like the rest, entirely dependent upon being provided with a good bike on which to race. If he doesn't have one, he is as lost as anyone else would be in the mid-pack.